Hi Tom,
I'm just an old guy and by no means an expert but I've built a Mendel from a kit and got it working quite well so I'll help if I can.
First off, is the picture you posted taken from the top of one side?
What do you mean "the first few layers go down perfectly with no clicking sound"? Are you saying that when it goes wrong, there is a clicking sound? If so, where from?
I'll assume that you have built the thing so that it's all level and square. If not, double check everything. Have you done all the basic calibrations? Have you got the Z axis homing properly? Have you calibrated the extruder?
Ian